Dear,

May I know the difference between the txi$counts and txi$abundance when the countFromAbundance is set to true(scaledTPM or lengthScaledTPM or dtuScaledTPM)? If set to xxxTPM, the txi$counts is still the raw counts value, right? As it's so close to the value when countFromAbundance is set to no.

Thanks a lot!

Have you read the vignette? Or the help page?

Here's what the help page for tximport says.

countsFromAbundance: character, either "no" (default), "scaledTPM",
          "lengthScaledTPM", or "dtuScaledTPM". Whether to generate
          estimated counts using abundance estimates:

            * scaled up to library size (scaledTPM),

            * scaled using the average transcript length over samples
              and then the library size (lengthScaledTPM), or

            * scaled using the median transcript length among isoforms
              of a gene, and then the library size (dtuScaledTPM).

          dtuScaledTPM is designed for DTU analysis in combination with
          'txOut=TRUE', and it requires specifing a 'tx2gene'
          data.frame. dtuScaledTPM works such that within a gene,
          values from all samples and all transcripts get scaled by the
          same fixed median transcript length. If using scaledTPM,
          lengthScaledTPM, or geneLengthScaledTPM, the counts are no
          longer correlated across samples with transcript length, and
          so the length offset matrix should not be used.

That seems pretty clear to me, but perhaps you have a particular question about something that isn't clear to you?